Primary effusion lymphoma is an aggressive lymphoma arising in the setting of HIV and HHV8 that primarily involves body fluids. Multicentric Castlemans disease is a non-clonal proliferative process that arises in the same clinical setting. Morphological diagnosis is difficult in these rare diseases. We have developed clinical flow cytometric assays that can aid in the diagnosis of primary effusion lymphoma and multicentric Castlemans disease, providing key clinical support to patients on NCI protocols. Involvement of the cerebrospinal fluid (CSF) by hematopoietic malignancies may also be difficult to document by morphology alone. In a study comparing morphology alone to morphology with flow cytometry, we demonstrated that flow cytometric immunophneotyping was useful in establishing a diagnosis of neoplasia in a series of patients with known lymphoma or leukemia and an initial diagnosis of atypical or suspicious CSF using morphologic criteria. The Flow Cytometry Unit evaluated the role of flow cytometric analysis in staging and management of patients with high grade B cell lymphomas. Flow cytometry identified neoplastic clones that constituted as little as 0.02% of total CSF lymphocytes. Flow cytometry detected involvement where cytology, chemistry and cell counts failed. Flow cytometric detection of disease was a negative prognostic factor and now prompts therapeutic intervention. As a result of the study it is recommended that patients at risk for CNS involvement by aggressive B cell lymphoma undergo staging CSF evaluation by flow cytometry. The Flow Cytometry Unit participated in an international consensus conference to determine optimal methodology for flow cytometric analysis of CSF.